Transcriptome characterization by RNA-Seq reveals the involvement of the complement components in noise-traumatized rat cochleae

Abstract

Acoustic trauma, a leading cause of sensorineural hearing loss in adults, induces a complex degenerative process in the cochlea. Although previous investigations have identified multiple stress pathways, a comprehensive analysis of cochlear responses to acoustic injury is still lacking. In the current study, we used the next-generation RNA-sequencing (RNA-seq) technique to sequence the whole transcriptome of the normal and noise-traumatized cochlear sensory epithelia (CSE). CSE tissues were collected from rat inner ears 1 d after the rats were exposed to a 120-dB (sound pressure level) noise for 2 h. The RNA-seq generated over 176 million sequence reads for the normal CSE and over 164 million reads for the noise-traumatized CSE. Alignment of these sequences with the rat Rn4 genome revealed the expression of over 17000 gene transcripts in the CSE, over 2000 of which were exclusively expressed in either the normal or noise-traumatized CSE. Seventy-eight gene transcripts were differentially expressed (70 upregulated and 8 downregulated) after acoustic trauma. Many of the differentially expressed genes are related to the innate immune system. Further expression analyses using qRT-PCR confirmed the constitutive expression of multiple complement genes in the normal organ of Corti and the changes in the expression levels of the complement factor I (Cfi) and complement component 1, s subcomponent (C1s) after acoustic trauma. Moreover, protein expression analysis revealed strong expression of Cfi and C1s proteins in the organ of Corti. Importantly, these proteins exhibited expression changes following acoustic trauma. Collectively, the results of the current investigation suggest the involvement of the complement components in cochlear responses to acoustic trauma.

Immune defense is the primary function associated with the differentially expressed genes in the cochlea following acoustic trauma

“…We had previously reported the transcriptional profile of the rat samples (Patel et al, 2013). In that study, the sequence reads were aligned to rn4 (Rat Genome Sequencing Consortium).…”

“…The RNA-sequencing analyses were performed to define the expression profile of the cochlear genes using a protocol that has been described in our previous publication (Patel et al, 2013). The total RNAs were extracted from the sensory epithelia using a Qiagen RNeasy Micro or Mini kit (Qiagen GmbH, Hilden, Germany) according to the manufacturer’s protocol.…”

“…Using RNA-sequencing, we have examined the noise-induced transcriptional changes of the cochlear genes in the rat (Patel et al, 2013). This comprehensive expression analysis identified a group of differentially expressed genes.…”

High-Throughput Technologies for Gene Expression Analyses: What We Have Learned for Noise-Induced Cochlear Degeneration

“…We have used the RNA-seq technique to determine the transcriptome of normal cochlear sensory epithelium and differentially expressed genes after acoustic trauma (Patel et al, 2013b). Our sequencing experiment revealed an average of 176 ± 21 million reads for the normal samples collected from the rat cochlea.…”

“…Studies have identified various stress conditions, including oxidative stress, apoptotic responses, ischemia, and energy exhaustion. In contrast to these pathological responses, molecular analyses have revealed complex signaling transduction involving multiple molecular pathways (Cho et al, 2004; Patel et al, 2013b; Taggart et al, 2001). It is expected that future systematic analyses of the global changes in gene expression will generate a complete data set for understanding the molecular mechanisms of noise-induced cochlear degeneration.…”